Commit 718f4bd1 authored by Aflitos, Saulo Alves's avatar Aflitos, Saulo Alves
Browse files

Fixed some small errors.

parent 71f407d4
......@@ -16,7 +16,7 @@ do
done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
# Use a single file for logging, use the starttime as identifier
LOGFILE="kmerfreq_heinz."`date +%Y%m%d_%k%M%S`.out
LOGFILE="FRC_heinz."`date +%Y%m%d_%k%M%S`.out
# Input assembly
#allpaths /home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
......@@ -27,12 +27,12 @@ LOGFILE="kmerfreq_heinz."`date +%Y%m%d_%k%M%S`.out
ASSEMBLY=/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
PREFIX=allpaths_lg
$MIN_PE_INS=320
$MAX_PE_INS=430
$MIN_MP_INS=2435
$MAX_MP_INS=3555
$ESTIMATED_GENOME_SIZE=760000000
$OUTPUT_HEADER=${PREFIX}.FRC.
MIN_PE_INS=320
MAX_PE_INS=430
MIN_MP_INS=2435
MAX_MP_INS=3555
ESTIMATED_GENOME_SIZE=760000000
OUTPUT_HEADER=${PREFIX}.FRC.
# Map reads against assembly with BWA
# Create index
......@@ -68,7 +68,10 @@ fi
# Create SAM files of the paired mappings
for name in rc_3018DAAXX_2 rc_30THBAAXX_2
do
bwa sampe -P ${PREFIX} ${PREFIX}.${name}_f.sai ${PREFIX}.${name}_r.sai ${name}_f.fastq ${name}_r.fastq > ${PREFIX}.${name}.sam
bwa sampe -P ${PREFIX} \
${PREFIX}.${name}_f.sai ${PREFIX}.${name}_r.sai \
${name}_f.fastq ${name}_r.fastq \
> ${PREFIX}.${name}.sam
# Convert result to BAM
samtools view -S ${PREFIX}.${name}.sam -b > ${PREFIX}.${name}.bam
# Sort the BAM
......@@ -78,7 +81,8 @@ fi
done
# Merge the created BAMs
samtools merge -r -1 ${PREFIX}.MP.bam ${PREFIX}.rc_3018DAAXX_2.sorted.bam ${PREFIX}.rc_30THBAAXX_2.sorted.bam
# The PE data : /home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/*.64.fastq
# PE data
# Map PE reads
for file in /home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/sample_R1_001.64.fastq /home/assembly/dev_150/sample_heinz/raw/illumina/PE_500/sample_R2_001.64.fastq
do
......@@ -97,8 +101,8 @@ fi
samtools sort ${PREFIX}.PE.bam ${PREFIX}.PE.sorted
# Index the BAM
samtools index ${PREFIX}.PE.sorted.bam
# run FRC
# run FRC as per README
FRC --pe-sam ${PREFIX}.PE.sorted.ba \
--pe-min-insert $MIN_PE_INS \
--pe-max-insert $MAX_PE_INS \
......@@ -108,5 +112,7 @@ FRC --pe-sam ${PREFIX}.PE.sorted.ba \
--genome-size $ESTIMATED_GENOME_SIZE \
--output $OUTPUT_HEADER \
# TODO : Create better CE statisitcs
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